Bioinformatics has evolved as a great tool for molecular biologists. There are various tools available for helping in reducing the time required to analyze biological materials be it DNA, RNA, Proteins etc. I wish to list here few of the commonly used tools. Please send me suggestions to improve the content. If you like or dislike something, let me know, your inputs matters. contact me: drsanjivk[at]gmail[dot]com

Bioinformatics Tools

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Wednesday, January 29, 2014

LINUX BASICS FOR BEGINNERS AND ADVANCE USERS

Since long I was trying to learn Linux. I
realized it is not as difficult as it seems. I have compiled some of the
basic commands that are mandatory to learn to step into this beautiful world.
They are not all, I have skipped grep, awk and sed knowingly, as I presume they deserve bit more attention. I will keep updating the list as soon as I can. Do
look around too, some good video tutorials are also available that aid in
learning. Also, I have made this available as a simple printable PDF. LINUX BASICS FOR BEGINNERS - Download HereLINUX BASICS FOR ADVANCE USERS - Download Here

Basic commands: On the terminal type these commands at-least
two-three times to practice. Also, it is advisable to read man (help) pages of
all these commands at least once.

#######################################################

Command

Function

man <command>

:

Displays
manual or help page for a commend, always read it full at least once

cd

:

Change
directory, to navigate from one directory to another

cd -

:

Toggle
between previous directory and current directory

ls

:

List files
or folders, with several arguments give detail information about the files
and folders, try: ls -ltrh

Word count,
can be combined (piped through) various other commands (it gives results as
lines, words and characters)

wc -c

:

Counts the
number of bytes

wc -w

:

Counts the
number of words

wc -l

:

Counts the
number of lines

free -m

:

Free memory
(ram) in mb

free -g

:

Free memory
(ram) in gb

df

:

Disk space

du - sch <dir>

:

Disk space
of the current directory

du -sch *

:

Disk space
of individual files or directories

du -sch * | sort -nr

:

Disk space
of individual files or directories sorted by file size

w

:

Who is
logged onto the system and what are they doing

ps

:

Processes
running by the users

ps -e

:

All the
processes running in the system, also used with argument -a, -x, read man ps

ps -o %t -p <pid>

:

How long the
process was running

ctrl+z

:

Suspend or
sleep the current running process in foreground

bg

:

Run process
in background

fg

:

Bring
processes foreground, those running in background

kill <pid>

:

Kills a
process with the given process id

kill -9 <pid>

:

Violently
kills a given process id giving it no time to cleanup

kill -l <pid>

:

List all
signals that can be sent to a process

kill -s sigstop <pid>

:

Suspends or
sleep a process

kill -s sigcont <pid>

:

Resumes or
wakes up a process

renice -n <value> <pid>

:

Gives a
priority value to the process id, ranges from 1-19, higher the value lower
the priority, default is 10, it is said to be how nice the process is i.e.
How much ram it leaves for other process to run

cmp <file1> <file2>

:

Compares two
given files

diff <file1> <file2>

:

Find the
differences between two files, compares two files, argument -w ignores
whitespace

mount

:

Mounts
drive, usage: mount /media/usb

umount

:

Unmounts
drive, usage: /media/usb

eject

:

Ejects cd
rom, usage: /media/cdrom

join

:

Combines
lines from two files on a common field, usage: join file1.txt file2.txt

tr a-z A-Z < file.txt

:

Transfers
case to another i.e. Lowercase to uppercase

tr A-Z a-z < file.txt

:

Transfers
case to another i.e. Uppercase to lowercase

xargs

:

Takes output
of one command and passes it as an argument to another command usage: cat
urllist.txt | xargs wget -c

Used to
display only specific columns from a text file or other command outputs i.e.
To display first field from a colon delimited file : cut -d: -f 1 file.txt ;
to display first and third field from colon delimited file : cut -d: -f 1, 3
file.txt

Used either
to check the status or properties of single file or file system, usage: stat
/etc/file.txt ; argument -f i.e. Stat -f / (displays the status of the file
system i.e. Size/total/free/available

ac -d

:

Displays the
statics about the user connect time, argument -d breaks the output for
individual days, usage: ac -d username

&

:

At the end
of the command executes job in the background but if you logout the job will
be killed

nohup

:

At the
beginning of the command executes job in background with (ampercent &),
usage: nohup ./script.sh & ; the job will run in background even if you
logout

screen

:

Once you
logout the same session will not be connected, to do that, end with screen
and attach it later by screen to get back as it was when you logged out